2016-12-10T03:14:59ZProduction of Ceratonova shasta Myxospores from Salmon Carcasses: Carcass Removal Is Not a Viable Management Optionhttp://hdl.handle.net/1957/59569
Production of Ceratonova shasta Myxospores from Salmon Carcasses: Carcass Removal Is Not a Viable Management Option
Foott, J. S.; Stone, R.; Fogerty, R.; True, K.; Bolick, A.; Bartholomew, J. L.; Hallett, S. L.; Buckles, G. R.; Alexander, J. D.
Severe infection by the endemic myxozoan parasite, Ceratonova (synonym, Ceratomyxa) shasta, has been associated with declines in and impaired recovery efforts of populations of fall-run Chinook Salmon Oncorhynchus tshawytscha in the Klamath River, California. The parasite has a complex life cycle involving a polychaete worm host as well as a salmon host. Myxospore transmission of this parasite, from salmon to polychaete, is a life cycle step during which there is a potential for applied disease management. A 3-year data set on prevalence, intensity, and spore characteristics of C. shasta myxospores was obtained from adult Chinook Salmon carcasses surveyed in the main stem of the Klamath River and three of its tributaries, Bogus Creek and the Shasta and Trinity rivers. Annual prevalence of myxospore detection in salmon intestines ranged from 22% to 52%, and spore concentration values per intestinal scraping ranged from 3.94 × 10² to 1.47 × 10⁷ spores. A prevalence of 7.3% of all carcasses examined produced >5.0 × 10⁵ spores, and these carcasses with “high” spore counts accounted for 76–95% of the total spores in a given spawning season. Molecular analysis of visually negative carcasses showed that 45–87% of these samples had parasite DNA, indicating they contained either low spore numbers or presporogonic stages of the parasite. Myxospores were rarely found in carcasses of freshly spawned adults but were common in decomposed carcasses of both sexes. The date of collection or age (based indirectly on FL) did not influence detection. The longer prespawn residence time for spring-run Chinook Salmon compared with that for fall-run Chinook Salmon in the Trinity River was associated with higher spore loads. The dye exclusion method for assessing spore viability in fresh smears indicated an inverse relationship in spore integrity and initial spore concentration. A carcass-removal pilot project in Bogus Creek for 6 weeks in the fall of 2008 (907 carcasses removed) and 2009 (1,799 carcasses removed) failed to measurably influence the DNA quantity of C. shasta in targeted waters. Combined with the high numbers of carcasses that contributed myxospores, we therefore deemed that this labor-intensive approach is not a viable management option to reduce the infectivity of C. shasta in Chinook Salmon in the Klamath River.
To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/uahh20/current
2016-01-01T00:00:00ZStructural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp WA102http://hdl.handle.net/1957/59540
Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp WA102
Brown, Nathan M.; Mueller, Ryan S.; Shepardson, Jonathan W.; Landry, Zachary C.; Morré, Jeffrey T.; Maier, Claudia S.; Hardy, F. Joan; Dreher, Theo W.
Background:
Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013 and maintained in non-axenic culture.
Results:
The Anabaena sp. WA102 5.7 Mbp genome assembly has been closed with long-read, single-molecule sequencing and separately a draft genome assembly has been produced with short-read sequencing technology. The closed and draft genome assemblies are compared, showing a correlation between long repeats in the genome and the many gaps in the short-read assembly. Anabaena sp. WA102 encodes anatoxin-a biosynthetic genes, as does its close relative Anabaena sp. AL93 (also introduced in this study). These strains are distinguished by differences in the genes for light-harvesting phycobilins, with Anabaena sp. AL93 possessing a phycoerythrocyanin operon. Biologically relevant structural variants in the Anabaena sp. WA102 genome were detected only by long-read sequencing: a tandem triplication of the anaBCD promoter region in the anatoxin-a synthase gene cluster (not triplicated in Anabaena sp. AL93) and a 5-kbp deletion variant present in two-thirds of the population. The genome has a large number of mobile elements (160). Strikingly, there was no synteny with the genome of its nearest fully assembled relative, Anabaena sp. 90.
Conclusion:
Structural and functional genome analyses indicate that Anabaena sp. WA102 has a flexible genome. Genome closure, which can be readily achieved with long-read sequencing, reveals large scale (e.g., gene order) and local structural features that should be considered in understanding genome evolution and functio
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central. The published article can be found at: http://bmcgenomics.biomedcentral.com/
2016-06-13T00:00:00ZNitrification Responses of Soil Ammonia-Oxidizing Archaea and Bacteria to Ammonium Concentrationshttp://hdl.handle.net/1957/59538
Nitrification Responses of Soil Ammonia-Oxidizing Archaea and Bacteria to Ammonium Concentrations
Giguere, Andrew T.; Taylor, Anne E.; Myrold, David D.; Bottomley, Peter J.
Although ammonia-oxidizing archaea (AOA) and bacteria (AOB) coexist in most non-acidic agricultural soils, the factors that influence their relative contributions to soil nitrification activity remain unclear. A 2- to 4-d whole soil microcosm assay was developed, utilizing the aliphatic C₈ alkyne 1-octyne to inactivate AOB-driven nitrification activity without impacting AOA nitrification activity. Responses of AOA- and AOB-supported net nitrification activities (accumulation of NO₂⁻ + NO₃⁻) to different concentrations of extractable NH₄⁺ were examined in four diverse, paired cropped and non-cropped Oregon soils sampled in summer and winter. Maximum AOA-supported net nitrification rates were significantly higher in non-cropped (3.7 mg N kg⁻¹ soil d⁻¹) than in cropped soils (0.9 mg N kg⁻¹ soil d⁻¹) and in summer (3.1 mg N kg⁻¹ soil d⁻¹) compared with winter soils (1.6 mg N kg⁻¹ soil d⁻¹). The NH₄⁺ concentration required to significantly stimulate AOB nitrification activity was significantly higher in cropped soils (67 mg N kg⁻¹ soil) than in non-cropped soils (12 mg N kg⁻¹ soil). Maximum AOB activity was significantly higher in cropped (8.6 mg N kg⁻¹ soil d⁻¹) than in non-cropped soils (2.9 mg N kg⁻¹ soil d⁻¹) and in summer (7.8 mg N kg⁻¹ soil d⁻¹) compared with winter soils (3.8 mg N kg⁻¹ soil d⁻¹). This study revealed that AOA- and AOB-supported nitrification rates in cropped and non-cropped soils respond differently to season and NH₄⁺ concentration and raises the possibility that AOA and AOB nitrification activities might be differentially managed to improve N use efficiency.
This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the Soil Science Society of America in cooperation with the American Society of Agronomy and Crop Science Society of America. It can be found at: https://dl.sciencesocieties.org/publications/sssaj/abstracts/79/5/1366; Access to this item has been restricted by repository administrators at the request of the publisher, the Soil Science Society of America, until March 01, 2017.
2015-10-02T00:00:00ZPersistence of Triploid Grass Carp in Devils Lake, Oregonhttp://hdl.handle.net/1957/59513
Persistence of Triploid Grass Carp in Devils Lake, Oregon
Clemens, Benjamin J.; Spangler, John J.; Robertson, Paul L.; Galovich, Gary M.; Banner, Craig R.; Gunckel, Stephanie L.; Ketchum, Lindsay L.; Bowden, R. Kanani; Spagnoli, Sean T.; Kent, Michael L.; Kirk, James P.
Grass carp Ctenopharyngodon idella are sometimes used as a biological tool for managing aquatic vegetation in reservoirs. Sterile, triploid fish were stocked in Devils Lake, Oregon, during 1986, 1987, and 1993 to control aquatic vegetation. We present a case study for using multiple measures on the same fish to determine whether illegal stocking of fertile, diploid grass carp occurred. An investigation into the estimated age of a dead grass carp found in Devils Lake suggested that it was significantly younger than would otherwise be expected, given the only stocking events occurred during 1986, 1987, and 1993. To determine whether illegal stocking or reproduction by presumed sterile grass carp had occurred in Devils Lake, we conducted a study that balanced the needs of lethally sampling grass carp for biological measures with the socially and politically sensitive sentiment of the pro–grass carp citizenry of Devils Lake. These considerations, in combination with a low catch per-unit effort, resulted in a modest sample size for grass carp. We sampled grass carp and recorded multiple measures for each fish. Ploidy testing of blood samples indicated the grass carp were all triploid. Based on gonadal histopathology, six fish were male, two were female, and two were sex-indeterminate with severe gonadal dysgenesis. Age estimates from lapillus otoliths were consistent with fish originating from the legal stocking events in Devils Lake. The grass carp were 21–30 y old, and we were unable to find published reports of grass carp anywhere else in the world that are older. The grass carp were significantly smaller than much younger fish from other regions. The small size of these grass carp relative to their age in Devils Lake suggests food limitations that stunted growth. The dead grass carp that was the impetus for this study was aged by anatomical structures that we have since found to be unreliable. This suggests that the dead grass carp was probably in fact older and originated from the legal stockings. The use of multiple biological measurements on a modest sample size of grass carp, combined with the knowledge that no juvenile grass carp have been observed since legal stocking occurred, lead us to conclude that the grass carp in Devils Lake are sterile fish that originated from legal stocking events.
To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is published by the U.S. Fish & Wildlife Service and can be found at: http://fwspubs.org/. All material appearing in the Journal of Fish and Wildlife Management is in the public domain and may be
reproduced or copied without permission unless specifically noted with the copyright symbol.; Supplementary material is available online at: http://www.fwspubs.org/doi/suppl/10.3996/042015-JFWM-044
2016-06-01T00:00:00Z